I have a little issue with a batch of H.E. stained images. The contrast between cell nuclei and matrix isn’t good enough to just set a colour threshold and then run “analyze particle” to get all the nuclei and positions like I normally do. I am interested in getting the position of all the single cells in a cluster of cells without loosing single cells in the normal tissue. Watershed doesn’t really help to separate them and I tried to use the weka segmentation tool (this worked for small images but with my 1 GB files and especially the darker stained sections it didn’t work). Do you have any suggestions what I can try?
thanks in advance,